Summary of Work: Improved understanding of the structure of HIV proteins can be useful in unraveling the function of the proteins and in understanding the mechanisms of the function of these proteins. This structural knowledge can also be useful in designing novel anti-HIV agents. X-Ray crystallography is the most accurate technique for determination of protein structures. Major drawbacks of the technique, however, are that it can be very time consuming and is dependent on the availability of protein crystals. Molecular modeling programs, on the other hand, can provide insights into the protein structure based on, amongst other things, homology with proteins whose structures are known. Although this approach is attractive, the results have often been less reliable than desired because insufficient information about the protein is available or the degree of homology with proteins of known structure is less than needed for the development of an accurate model. If information such as which amino acid residues are on the surface of the protein is available, however, the quality of the computer generated model can be significantly increased. This project is designed to probe the primary and tertiary structures of HIV proteins using a combination of chemical modifications, enzymatic degradations and mass spectrometric identification.We have characterized the heterogeneity of the glycans on rgp120 using a combination of MALDI/MS and nanoelectrospray/MS/MS. This information was used along with the known structure of a truncated gp120 to model a structure of the intact, fully glycosylated gp120. From this model we observed that the surface glycans are spatially segregated so that high mannose are clustered together as are the complex glycans.We have investigated the interactions of gp120 with potential anti-HIV DNA based drugs using affinity capillary electrophoresis with laser induced fluorescence detection. We found that phosphorothioate oligodeoxynucleotides containing four contiguous guanosine residues bind well and that increased chain length increases binding with gp120.